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Last year, activists in California collected 1 million signatures to put the California Right to Know Genetically Engineered Food Act on the November 2012 ballot. Named Proposition 37, the measure sought to make California the nation’s first state to require the labeling of foods that included genetically modified organisms (GMO).

Given California’s size and national influence, Prop 37’s passage threatened to unleash a labeling rush upon the country’s food providers and ensure that similar legislation would find its way in front of voters across the U.S. On Election Day, however, Californians rejected the measure 53 to 47 percent, a result facilitated by an estimated $46 million push from a coalition of farmers, grocers, and food companies—including restaurant-industry stalwarts like PepsiCo, Unilever, Coca-Cola, and Kraft Foods—who opposed the legislation.

While Prop 37’s opponents might have exhaled a sigh of relief following its defeat, the California measure still captured the nation’s attention and thrust GMOs onto consumers’ radars.

On November 6, 2012, the day of the Prop 37 vote, Just Label It chairman Gary Hirshberg wrote in a Huffington Post editorial that California’s “Yes on 37” campaign had raised the profile of GMOs far beyond California’s borders and warned: “This battle is just warming up.”

Nearly a year later, Hirshberg’s words seem prophetic. High-profile food activists are rallying against the use of GMOs, and more consumers are questioning whether to buy foods that use them. And, having answered customers’ cries for less sodium, trans fats, and high fructose corn syrup in menu items, quick-service operators are starting to hear rumblings of an anti-GMO sentiment.

Earlier this year, Connecticut passed the nation’s first GMO-labeling law, albeit with an important caveat for the 3.6 million–resident state: The legislation would only become active if other Northeastern states jumped on board with similar provisions.

As it stands, more than two dozen states—including some of Connecticut’s New England neighbors—are crafting GMO-labeling laws.

The GMO discussion isn’t limited to the state capitol buildings. At Abbott Laboratories’ annual meeting in April, shareholders voted on a resolution to remove GMOs from the company’s nutritional products, including Similac infant formula. Though Abbott shareholders rejected the proposal, the vote further underscored the expanding target on GMOs.

Developed in 1973, GMOs are organisms in which the genetic material, or DNA, has been altered in a way that does not occur naturally. More to the point for food, GMOs use controlled, specific biotechnology to expedite the process of creating stronger, healthier, and more productive crops.

GMOs were developed and remain in use for good reason: Such crops produce higher yields with less fertilizer and pesticide input, and reduce the impact of drought and high temperatures on plant growth. Furthermore, genetically engineered crops help agriculture stay ahead of the climate-change curve and ensure more efficient use of land and water to feed the world’s booming population. Biotech scientists are now working on enhancing the nutritional value of GMO crops, improving taste and color, and keeping food fresh longer to reduce waste.

“The science is only moving forward,” says Dr. Ruth MacDonald, chair of the food science and human nutrition department at Iowa State University.

In fact, GMO technology has helped the world through several crises.

When the papaya ringspot virus threatened the entirety of the world’s papaya crop in 1980, a genetically modified variety rescued the crop. In 2000, the Rockefeller Foundation teamed with the International Rice Research Institute to develop a new rice seed that could deliver sorely needed vitamin A to people in developing nations. And one of the first GMO products to market, insulin, now aids thousands of Americans battling diabetes.

GMOs’ historical success and celebrated agricultural benefits, however, have failed to silence the growing number of critics. Concerns about GMOs run from human health and environmental risks to economic and philosophical questions, often setting up the perceived battle between the consumer’s health and the farmer’s wealth.

“This is one of the things that rubs people the wrong way,” MacDonald says.

Some have called GMOs morally irresponsible and attribute genetically engineered food to conditions such as obesity, cancer, infertility, genetic defects, and the prevalence of food allergies. These complaints have intensified the GMO debate. But what remains scary to most about GMOs is even simpler: the unknown.

Credible long-term studies on GMOs remain elusive, while the name itself proves frightening. After all, it’s one thing to discuss genetics and DNA when it comes to cancer or diabetes, but quite another to apply those words to the dinner table. Some, in fact, have dubbed GMOs “Frankenfood.”

According to the U.S. Department of Agriculture’s (USDA) Economic Research Service, the adoption of genetically engineered crops in the U.S. has risen steadily in the 21st century. In 2000, about 54 percent of soybeans’ planted acres were genetically engineered; today, that number is 93 percent. GMO corn has experienced an even more dramatic rise, moving from 25 percent in 2000 to 90 percent in 2013.

During this explosion, no red flags have been raised regarding GMOs’ effects on health, according to a 2012 report on GMOs from the American Medical Association’s (AMA) Council on Science and Public Health. “Bioengineered foods have been consumed for close to 20 years, and during that time, no overt consequences on human health have been reported and/or substantiated in the peer-reviewed literature,” the report’s executive summary said.

In 1992, the U.S. Food and Drug Administration (FDA) enacted a policy of substantial equivalence, effectively saying that the GMO process does not change food composition. More than two decades later, the FDA maintains that stance, seeing no reason to acquiesce to the GMO outcry.

The fear that consumed DNA can pass into human cells is unrealistic, says MacDonald, herself a self-described concerned mother and consumer. She says modifying plant and animal genetics is a long-held agriculture practice that has simply been made faster and more specific by modern DNA technology. She calls the GMO fear “unjustified.”

“The DNA you consume is not getting absorbed into your DNA and will not affect your personal genomic makeup,” MacDonald says.

Finally, there’s the lingering concern that GMOs are created behind closed doors with little oversight and control. This isn’t the case, MacDonald says. Before any GMO crop or animal—only salmon is being considered thus far—is approved for human consumption, exhaustive testing must show no human or environmental risk; that data is then monitored by the FDA, Environmental Protection Agency (EPA), and the USDA’s Animal and Plant Health Inspection Service.

“There are strong checks and balances, and it takes years for a GMO’s safety and value to be tested before it enters the food supply,” MacDonald says.

“It’s unfortunate that people are afraid of GMOs, because there is no logical reason for them to be feared.”

An ongoing battle

Despite scientists’ GMO approval, concerns over the organisms continue to mount in the U.S. Some critics have called for mandatory GMO labeling, as is the case in dozens of nations around the globe, including Russia, Japan, and throughout Europe, while others have lobbied for the total elimination of GMOs from the nation’s food supply.

Now the debate is trickling into the quick-service industry.

Chipotle became an early and vocal advocate for Prop 37. Addressing the legislation on its website, the Denver-based chain said: “We want our customers to know exactly what they are eating. For us, this is real transparency—because knowing more about where our food comes from is always better than knowing less.”

Chipotle’s support for Prop 37 morphed into action this summer, when the fast-casual giant became the first national chain to label GMOs in its food.

On its website, Chipotle specifically identifies the genetically modified ingredients in each menu item.

“We believe in transparency in our food system … and we’ve favored a food system that emphasizes care over chemistry,” says Chris Arnold, Chipotle’s spokesman.

Chipotle isn’t the only big food brand to enter the GMO ring. Grocer Whole Foods has pledged to label all of its GMO products by 2018, the first national grocery chain to set a deadline for full GMO transparency.

Companies opposing GMO labeling have largely done so on the basis that such a measure would create unnecessary confusion and lead consumers to view the label as a sign of risk. Some industry observers have compared GMO labeling to putting a skull and crossbones on a product.

The AMA’s 2012 report supported the FDA’s science-based policies that “do not support labeling without evidence of material differences between bioengineered foods and their traditional counterparts.”

(The Council on Science and Public Health did, however, express a desire for mandatory pre-market safety assessments, while advising consumers wishing to purchase non-GMO foods to seek out the USDA Organic label.)

Given logistical challenges and the associated costs, MacDonald says, GMO labeling is an unrealistic goal. While she concedes that labeling is a noble purpose when it conveys nutritional value and allergen warnings, she says GMO labeling grows complicated when the discussion moves from an end product to the production method. For instance, many of the products obtained from GMO corn (corn oil or corn starch) have no traces of the GMO gene or protein and, as such, there exists no way to verify that these products came from a GMO plant.

Additionally, if GMO soybeans were fed to an animal, it begs the question of whether or not the meat or milk from that animal is considered GMO.

“Making GMO labeling required would be a fruitless waste of resources,” MacDonald says. “Foods that have ingredients from GMO products or from animals fed GMO grains are so ubiquitous in the U.S. that almost everything would be labeled.”

GMOs moving forward

Isabel VanDerslice, outreach coordinator with the Non-GMO Project advocacy group, knows of no other restaurant chain except for Chipotle that is making GMO labeling or non-GMO kitchens an immediate priority. She says that any such efforts thus far have likely been curtailed by the complicated, ever-evolving nature of supply chains and the many companies and players that comprise those supply chains.

Arnold acknowledges that there exists no clear scientific consensus on the impact of GMOs, but he says Chipotle’s decision to label its GMO ingredients was easy to make and execute and served an earnest response to consumers’ sprouting interest in GMOs. Much more difficult, however, will be Chipotle’s next step: eliminating GMOs from its more than 1,400 restaurants. That process poses significant challenges given the prevalence of GMO crops and the fact that most non-GMO crops are either organic or exports.

“This means you’re either fighting for a limited supply and paying a significant premium to get it or you’re finding substitutes,” Arnold says.

Chipotle is working with its suppliers to remove GMOs or discover suitable substitutes, such as replacing GMO soybean oil with non-GMO sunflower oil or rice bran oil. While Arnold says there is no timeline to eradicate GMOs from Chipotle’s kitchens, the initiative has emerged as a greater priority over the last year. “We’ll keep working at it,” he says.

Like Chipotle, ice cream giant Ben & Jerry’s has announced its plan to remove GMOs from its products. The Unilever-owned company hopes to have that process accomplished by the end of this year.

Warady’s Enjoy Life Foods, however, has already hit that ambitious target. All of the 38 items that Enjoy Life Foods dispenses to more than 13,000 retail stores across North America and hundreds of foodservice outlets are independently verified non-GMO products.

“Big companies will say that this is too hard to do, but we’re a small company and we made it happen,” Warady says. “The roadmap is there.”

In the years ahead, Warady predicts, various states will require GMO labeling, escalating both awareness and the rate of change. With increased consumer and competitive pressure, he says, some quick-service restaurants will be encouraged to add non-GMO solutions to their menus.

“I don’t doubt for a second that some opportunistic chains will see the GMO conversation as a way to market better-for-you products,” Warady says. “In fact, I think we’re going to see a few chains get there very quick and others compelled to follow suit.”